5th June - the COVID-19 coronavirus compendium

Interacting with your existing social network, but avoiding others, helps to flatten the curve
Published in Microbiology
5th June - the COVID-19 coronavirus compendium

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This week we learnt that interacting with people similar to you, based on existing social networks, may allow lockdown to be lifted without greatly increasing the spread of the virus, further evidence that black and south Asian people in the UK are at an increased risk of SARS-CoV-2, and that the outbreak in New York City was caused by multiple introductions from Europe.


More studies continue to show that hydroxychloroquine is not an effective treatment for COVID-19. This time, researchers gave it to patients who self-reported that they had been exposed to someone who had tested positive for the virus, as post-exposure prophylaxis. There was no significant difference in the rates of people infected in the hydroxychloroquine group, versus the control group given a placebo. There were also no serious adverse effects in the 400 or so people hydroxychloroquine group, contrasting with some other reports.

Baricitinib inhibits cytokines and reduces levels of SARS-CoV-2 when grown in cell culture. It was also tested on four COVID-19 patients, but without a control group the results are hard to interpret.

Convalescent plasma from recovered patients did not lead to clinical improvement in a treatment group, compared to a control group. The study was small, with just 103 patients, and so larger studies are still warranted.

Social distancing

Flattening the curve can be achieved by clustering, so that groups of similar people remain isolated from other groups who are less similar, and live further away. Three different strategies for clustering are modelled: allowing contact with similar people; strengthening contact in communities; and repeatedly interacting with the same people in bubbles. Each worked effectively to reduce the spread of the virus in a model, and so can be used to inform policy as lockdown relaxes.

Non-pharmaceutical interventions in South Korea reduced the spread of the virus, without the need for a full lockdown.


Supply chain losses are related to the duration of the lockdown, rather than its strictness, in a model of various lockdown scenarios in different countries over time.

Risk of severe disease

Two studies looked at the increased risk of black and south Asian people in the UK testing positive for SARS-CoV-2, as well as having severe disease. The first study found that black and south Asian people were at a greater risk of testing positive for the virus, as well as more likely to be hospitalised. They also found that deprivation and lack of qualifications were associated with an increased risk of infection. The second study also found that black and south Asian people in the UK are at an increased risk of hospitalisation with COVID-19. The effect was still seen when other risk factors were controlled for including neighbourhood deprivation, household crowding, smoking, and body size.

Co-morbidities and age were associated with mortality from COVID-19 in Michigan, with hypertension and diabetes most commonly seen. Advanced age and lactate dehydrogenase levels were associated with risk of severe disease in China.

Obesity and diabetes are both risk factors for severe COVID-19 in Mexico, in a large study of more than 50,000 cases. Obesity was the main risk factor for severe disease and death of COVID-19 in New York, as well as in children who were ill with the virus. Newly diagnosed diabetes was shown to be a greater risk factor for severe COVID-19 than known diabetes.

Patients with cancer are more likely to have severe COVID-19, according to data from nine hospitals in Wuhan.


Elevated D-dimer was a predictor of in-hospital mortality in Wuhan. Obesity with lymphopenia was associated with a worse outcome in another study.


The ability of SARS-CoV-2 to grow in a variety of readily available cell lines was described. A US virus isolate has been made available for other researchers.

Polymorphisms in SARS-CoV-2 circulating in Iran were described. A website that allows users to visualise mutations in SARS-CoV-2 was developed.


A recombinant Lactobacillus plantarum strain expressing the SARS-CoV-2 spike protein was constructed.


There were multiple independent introductions of SARS-CoV-2 into New York City in March, according to an analysis of the viral genome from 84 patients. The majority of introductions were from Europe, showing that New York’s role as a transport hub led to the spike in cases, although clustering of genomes showed that there was early community spread. Many viral sequences were identical, showing that the virus is not mutating rapidly.

A cluster of cases of COVID-19 were associated with a shopping mall in Wenzhou, China, most likely from indirect transmission such as contamination of surfaces. Viral RNA was found on disposable wooden chopsticks used in a hospital. A US patient with COVID-19 had contact with fifty other people, but none of them tested positive for the virus, or for antibodies.

Children were much less likely than adults to catch SARS-CoV-2 in a household setting. Less than 3% of pregnant women in Seattle tested positive for SARS-CoV-2, once universal testing was implemented.

The reproductive number in Singapore was 0.7 in February and reduced further to 0.6 in March.

Mental health

Stay at home orders reduced online searches associated with mental health symptoms, including suicide ideation and anxiety.

An app to support the mental health of healthare professionals was developed and used in several countries.


Hospitalisation for acute heart failure declined during COVID-19, but symptoms were worse in those who attended hospital, according to data from Kings College Hospital in London. It is unclear if this is due to reduced incidence, or more likely less patients travelling to hospital during lockdown.

Half of the hospital rooms tested in Singapore showed contamination with SARS-CoV-2 RNA, and there was some evidence of aerosol spread. Viral RNA was detected in two hospitals in South Korea, although only in the patient’s room, not in adjacent areas. Detection of viral RNA does not imply live virus. Extra-hospital contacts without PPE were associated with risk of SARS-CoV-2 infection in healthcare staff in Brescia, Italy.

30% of US nursing homes had a COVID-19 case, with star ratings not associated with this risk. In Los Angeles, 19% of residents and 6% of staff at a nursing home tested positive for SARS-CoV-2.


Vaporized hydrogen peroxide was effective at decontaminating N95 respirators, so that they can be re-used up to three times, in this study that used live virus. UV light was also effective, heat less so. The filtration efficiency of various homemade facemasks was tested, with polypropylene spunbond the most effective.

Mental health

Older adults had a more optimistic outlook on COVID-19, despite their fears of a fatal infection, in a survey of more than 6000 in the US. Portuguese healthcare workers believe they are at a higher risk of infection than the general population, in a survey.


Dominant epitopes in the SARS-CoV-2 spike protein that are the target of antibodies were identified in the convalescent sera of COVID-19 patients. These could be the target for vaccines or antibody therapies.

Every single one of 70 COVID-19 patients developed neutralising antibodies against SARS-CoV-2 after 20 days. Those with a worse clinical outcome had higher levels of antibodies.


The flu season was smaller in East Asia during COVID-19, but not in the US or Europe, perhaps showing the relative effects of social distancing in those regions. A study looking at South Korea confirmed this. Influenza-like illness in New York City was tracked during the early phase of the outbreak, declining and then rising again.


Knowledge of COVID-19 varied depending on education, income, and race, showing that educational tools need to be developed with diverse communities in mind. 80% of Taiwanese people rely on the internet for COVID-19 information.


COVID-19 patients had a reduced bacterial diversity in their gut microbiome, when compared to uninfected controls of influenza H1N1 patients.


A high throughput screening test for SARS-CoV-2 was tested and shown to be specific and sensitive.

Clinical findings

Patients admitted to ICU in New York frequently had acute kidney injury. Other clinical findings are described in a case series of the first 1000 patients in the city. 20% of those hospitalised died. Almost a third of COVID-19 patients had elevated liver enzyme levels.

All of the children hospitalised with COVID-19 in Chicago had an underlying comorbidity or co-infection. 21 cases of Kawasaki disease shock syndrome were seen in children and adolescents in Paris; half were of African ancestry and all recovered.

SARS-CoV-2 RNA was detected in the milk of a mildly symptomatic mother with COVID-19, although live virus was not tested for.

Pernio-like lesions were reported in young people with relatively mild COVID-19, and parotitis (which means inflammation of the parotid salivary glands – I had to look it up) was seen in three COVID-19 patients in France.

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Go to the profile of Alexander E. Gorbalenya
about 4 years ago

very informative!